Home » 'Junk DNA' » Latest ENCODE Research Validates ID Predictions On Non-Coding Repertoire

Latest ENCODE Research Validates ID Predictions On Non-Coding Repertoire

Readers will likely recall the ENCODE project, published in a series of papers in 2007, in which (among other interesting findings) it was discovered that, even though the vast majority of our DNA does not code for proteins, the human genome is nonetheless pervasively transcribed into mRNA. The science media and blogosphere is now abuzz with the latest published research from the ENCODE project, the most recent blow to the “junk DNA” paradigm. Since the majority of the genome being non-functional (as has been claimed by many, including notably Larry Moran, P.Z. Myers, Nick Matzke, Jerry Coyne, Kenneth Miller and Richard Dawkins) would be surprising given the hypothesis of design, ID proponents have long predicted that function will be identified for much of our DNA that was once considered to be useless. In a spectacular vindication of this hypothesis, six papers have been released in Nature, in addition to a further 24 papers in Genome Research and Genome Biology, plus six review articles in The Journal of Biological Chemistry.

The lead publication of the finding (“An Integrated Encyclopaedia of DNA Elements in the Human Genome“) was released in Nature. The abstract reports,

“The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.” [emphasis added]

They further report that,

“[E]ven using the most conservative estimates, the fraction of bases likely to be involved in direct gene regulation, even though incomplete, is significantly higher than that ascribed to protein- coding exons (1.2%), raising the possibility that more information in the human genome may be important for gene regulation than for biochemical function. Many of the regulatory elements are not constrained across mammalian evolution, which so far has been one of the most reliable indications of an important biochemical event for the organism. Thus, our data provide orthologous indicators for suggesting possible functional elements.”

As this Nature press release states,

“Collectively, the papers describe 1,640 data sets generated across 147 different cell types. Among the many important results there is one that stands out above them all: more than 80% of the human genome’s components have now been assigned at least one biochemical function.” [emphasis added]

The UK Guardian also covered the story, noting that

“For years, the vast stretches of DNA between our 20,000 or so protein-coding genes – more than 98% of the genetic sequence inside each of our cells – was written off as “junk” DNA. Already falling out of favour in recent years, this concept will now, with Encode’s work, be consigned to the history books.” [emphasis added]

This new research places a dagger through the heart of the junk DNA paradigm, and should give adherents to this out-dated assumption yet further cause for caution before they write off DNA, for which function has yet to be identified, as “junk”. Be sure to also check out Casey Luskin’s coverage of the findings at ENV.

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68 Responses to Latest ENCODE Research Validates ID Predictions On Non-Coding Repertoire

  1. “This is going to make my life very complicated.”

    Larry Moran
    Encode Leader Syas that 80% of our Genome is Functional

    :-)

  2. This metaphor of junk isn’t that useful.

    Unless you’re a Darwinist.

  3. So what does this mean for modern evolutionary theory? That’s what I want to know. Please post any links that address this question.

    For example, isn’t it a claim of modern evolutionary theory that we can reliably determine evolutionary relationships from sections of non-functional DNA precisely because they are non-functional?

    (Not to be confused with their “I don’t think an intelligent designer wouldn’t have done it that way, therefore… “argument.”)

  4. A few notes. Here is a neat video on the announcement:

    Scientists go deeper into DNA (Video report) (Junk No More) – Sept. 2012
    http://bcove.me/26vjjl5a

    Here is a beaut of a quote on the question of functionality for the remaining remaining 20%:

    Junk No More: ENCODE Project Nature Paper Finds “Biochemical Functions for 80% of the Genome” – Casey Luskin September 5, 2012
    Excerpt: The Discover Magazine article further explains that the rest of the 20% of the genome is likely to have function as well:
    “And what’s in the remaining 20 percent? Possibly not junk either, according to Ewan Birney, the project’s Lead Analysis Coordinator and self-described “cat-herder-in-chief”. He explains that ENCODE only (!) looked at 147 types of cells, and the human body has a few thousand. A given part of the genome might control a gene in one cell type, but not others. If every cell is included, functions may emerge for the phantom proportion. “It’s likely that 80 percent will go to 100 percent,” says Birney. “We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful.”"
    http://www.evolutionnews.org/2.....64001.html

    But it was really not all that hard to see that we are NOT dealing with massive amount of junk in the DNA!

    Multidimensional Genome – Dr. Robert Carter – video (Notes in video description)
    http://www.metacafe.com/w/8905048

    3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell – Oct. 2009
    Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip — while avoiding the knots and tangles that might interfere with the cell’s ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication.
    http://www.sciencedaily.com/re.....142957.htm

    DNA – Replication, Wrapping & Mitosis – video
    https://vimeo.com/33882804

    here is physorg’s announcement:

    ENCODE project: In massive genome analysis new data suggests ‘gene’ redefinition – September 5, 2012
    Excerpt: The vast amount of data generated with advanced technologies by Gingeras’ group and others in the ENCODE project is likely to radically change the prevailing understanding of what defines a gene, the unit we routinely use, for instance, to speak of inheritable traits like eye color or to explain the causes of and susceptibility to most diseases, running the gamut from cancer to schizophrenia to heart disease.
    http://medicalxpress.com/news/.....-gene.html

    Actually a ‘redefinition of a gene’, despite the denial of Darwinists, was already being forced upon us:

    The Extreme Complexity Of Genes – Dr. Raymond G. Bohlin – video
    http://www.metacafe.com/watch/8593991/

    Here is the NY TIMES reporting on ENCODE announcement:

    Bits of Mystery DNA, Far From ‘Junk,’ Play Crucial Role – September 2012
    Excerpt: The system, though, is stunningly complex, with many redundancies. Just the idea of so many switches was almost incomprehensible, Dr. Bernstein said.
    There also is a sort of DNA wiring system that is almost inconceivably intricate.
    “It is like opening a wiring closet and seeing a hairball of wires,” said Mark Gerstein, an Encode researcher from Yale. “We tried to unravel this hairball and make it interpretable.”
    There is another sort of hairball as well: the complex three-dimensional structure of DNA. Human DNA is such a long strand — about 10 feet of DNA stuffed into a microscopic nucleus of a cell — that it fits only because it is tightly wound and coiled around itself. When they looked at the three-dimensional structure — the hairball — Encode researchers discovered that small segments of dark-matter DNA are often quite close to genes they control. In the past, when they analyzed only the uncoiled length of DNA, those controlling regions appeared to be far from the genes they affect.
    http://www.nytimes.com/2012/09.....wanted=all

    here is science daily’s release:

    First Holistic View of How Human Genome Actually Works: ENCODE Study Produces Massive Data Set – ScienceDaily (Sep. 5, 2012)
    Excerpt: “During the early debates about the Human Genome Project, researchers had predicted that only a few percent of the human genome sequence encoded proteins, the workhorses of the cell, and that the rest was junk. We now know that this conclusion was wrong,” said Eric D. Green, M.D., Ph.D., director of the National Human Genome Research Institute (NHGRI), a part of the National Institutes of Health. “ENCODE has revealed that most of the human genome is involved in the complex molecular choreography required for converting genetic information into living cells and organisms.”
    http://www.sciencedaily.com/re.....140913.htm

  5. A few more notes: Here is a bit of history on the Junk DNA argument by evolutionists

    Functionless Junk DNA Predictions By Leading Evolutionists
    http://docs.google.com/View?id=dc8z67wz_24c5f7czgm

    more tidbits

    What Is The Genome? It’s Not Junk! – Dr. Robert Carter – video – (Notes in video description)
    http://www.metacafe.com/w/8905583

    The Mysterious Epigenome. What lies beyond DNA? – Woodward – – video
    http://www.youtube.com/watch?v=RpXs8uShFMo

    Hopefully, one day soon, experts will do a study telling us exactly what ‘quantum computation’ is doing in DNA!

    Quantum Information/Entanglement In DNA – Elisabeth Rieper – short video
    http://www.metacafe.com/watch/5936605/

    Quantum entanglement between the electron clouds of nucleic acids in DNA – Elisabeth Rieper, Janet Anders and Vlatko Vedral – February 2011
    http://arxiv.org/PS_cache/arxi.....4053v2.pdf

    In the following article, Dr. Hameroff expands on the quantum computation aspect of Rieper, Anders and Vedral paper:

    Is DNA a quantum computer? Stuart Hameroff
    Excerpt: DNA could function as a quantum computers with superpositions of base pair dipoles acting as qubits. Entanglement among the qubits, necessary in quantum computation is accounted for through quantum coherence in the pi stack where the quantum information is shared,,,
    http://www.quantumconsciousnes.....puter1.htm

    Music, video, and Verse:

    Steven Curtis Chapman – Lord of the Dance (Live)
    http://www.youtube.com/watch?v=hDXbvMcMbU0

    Alexander Tsiaras: Conception to birth — visualized – video
    http://www.youtube.com/watch?v=fKyljukBE70

    Comment from preceding video: Mathematician and medical image maker Alexander Tsiaras offers a stunning visualization of the process that in nine months takes an emerging human life from conception to birth. He speaks of “the marvel of this information,” “the mathematical models of how these things are done are beyond human comprehension,” “even though I look at this with the eyes of mathematician I look at this and marvel. How do these instruction sets not make mistakes as they build what is us?”

    Psalm 139:13-14
    For you created my inmost being; you knit me together in my mother’s womb.
    I praise you because I am fearfully and wonderfully made; your works are wonderful, I know that full well.

  6. Well, well, well.

    We’ve had several threads over the past few months on this issue, with committed evolutionists proclaiming over and over that junk is pervasive, that the majority of DNA is junk, etc. What say you now? Crickets . . .

    Just to toot my own horn for a minute, I have publicly stated on more than one occasion on UD that no more than 5-10% of DNA would ultimately turn out to be non-functional. As far as I know, I haven’t seen anyone else on those threads be willing to make such a concrete assessment. We’re at 80% function now, so it is only a matter of time and a bit more research before we are above 90%.

    I would say “Told you so!” but that would be unsporting! :)

    —–

    This is a spectacular example of one paradigm making a major prediction and the other paradigm making a major prediction that is exactly the opposite. It is absolutely clear that the evolutionary paradigm has failed miserably and that the design prediction has been borne out.

    Will this kill off Darwinian evolution? Of course not. Because it is not based on evidence, but on a philosophical viewpoint. Design is excluded from consideration on philosophical/religious grounds and so the only thing that can be considered is some kind of (unspecified, undefined, unclear) cosmic accident over time.

  7. 7

    I can’t wait to hear how this “sheds new light on evolution”. Let the story-telling begin!

  8. I can’t wait to hear how this “sheds new light on evolution”.

    Oh, that’s good! Thanks!

  9. A few thoughts after reading the reportage of the literature.

    (a) The headline “80%” refers to “some chemical reaction”, and the Morans of this world are poining to a much lower 20% figure for “selectable function”, which is still far higher than expected. The authors, though, defend their terminology on the basis that much genuine function will prove non-selectable, and that one can’t decide something is not useful until you know what it does. So the argument looks more dispassionate if one understands and quotes both figures, since they both do the job of refuting “Junk DNA” (Of course, we all know that no biologist has use that inaccurate term for a DECADE or so. Francis Collins only used it in 2007 for theological reasons ;-).

    (b) If protein-coding genes are now a very small minority of the redefined genes, most of which are non-selectable switches for codong genes shared amongst many species, does population genetics actually mean anything much mathematically now?

    (c) If the size of the genome has been swelled to comprise mainly near-neutral elements, does there remain any significant role for natural selection? How can selection handle speciation if speciation is mainly switch configuration?

    (d) Much of the extended-genome is not conserved … ie it’s species-specific. What does that do for the rate at which evolution could happen, say between apes and man?

  10. The following ia a quote from Dennis Venema at BioLogos:

    “For example, we see the genes for air-based olfaction (smelling) in whales that no longer even have olfactory organs. Humans have the remains of a gene devoted to egg yolk production in our DNA in exactly the place that evolution would predict.”

    This is yet another prediction verified for evolution through common ancestry. I know that some on this board are not against evolution or common ancestry so I fail to see why the celebrations. ID proponents are saying this but so do Darwinists. It seems that ID believes it and yet celebrates when there is evidence against it. After all, wasn’t the prediction of pseudo genes a result of evolution through common ancestry? So if this is proof that it may not be the case, isn’t ID refuted too?

    I guess what I’m trying to say is that this is just proof to knock of a tip of the evidence iceberg but ID accepts the rest of the iceberg anyway. So what did this accomplish in the end?

  11. Here is a another video announcement of the ENCODE work:

    ENCODE: Encyclopedia Of DNA Elements – video
    http://www.youtube.com/watch?v=Y3V2thsJ1Wc

  12. For example, we see the genes for air-based olfaction (smelling) in whales that no longer even have olfactory organs.

    I thought that both air and water are fluids.

    I wonder what he thinks the difference is between fluid-based (air) olfaction and fluid-based (water) olfaction.

  13. “Humans have the remains of a gene devoted to egg yolk production in our DNA in exactly the place that evolution would predict.”

    Note the ‘would’ predict. I presume he doesn’t have an actual citation of someone predicting that long beforehand. And any instances of confirmed predictions are more a product of luck than any knowledge flowing from evolutionary theory.

    What typically happens is that we learn something new in biology that is interpreted in the paradigm of evolutionary thinking. Then if it matches, evolutionists say, “See, that’s what evolution would predict.” If it doesn’t match, the response is that evolution is messy, non-linear, makes changes all the time, and — surprise — that we shouldn’t expect to see the particular feature survive. This kind of illogic has been used over and over.

    The simple fact is that evolutionary theory makes very few bona fide predictions. Some things will evolve, some won’t; some features will be preserved, others won’t; some will survive, others won’t. Under the evolutionary paradigm, there is no reason for thinking that any feature of any species will survive through long periods of time. Evolutionary theory can be largely summed up with the following statement: Stuff happens.

  14. @JLAfan2001

    In those cases, I would imagine those genes perform more than one function, otherwise they wouldn’t be conserved for tens to hundreds of millions of years. According to wikipedia (typically hostile to our views):

    The yolk sac is a membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins.

    So the “yolk gene” is not a vestigal remnant. According to Whale ‘sense of smell’ revealed, 2010:

    The whales’ sense of smell was revealed when scientists dissected their bodies and found olfactory hardware linking the brain and nose, and functional protein receptors required to smell. Previously, whales and dolphins were thought to lack the ability. “Upon taking a brain out, I noticed that there were olfactory tracts, which, in other mammals, connect the brain to the nose,” Prof [Hans] Thewissen told the BBC. “I followed those to the nose, and noted that all the olfactory hardware is there.”

    Searching for the quote from Dennis Venema leads to Rachel Held Evans blog, which was published over a year after the BBC whale article. Why is he still using that argument?

  15. These developments are deadly to Darwinism (well as a theory it’s already a corpse, but propped up by its supporters despite the stench.)

    Kimura said the majority of the genome is selectively neutral. For humans that would mean most of the 4 giga base pairs were not under the influence of selection.

    Now that we find most of the 4 giga base pairs are functional, we have to deal with the fact that they are functional without the influence of selection. Hence we find complex features of biology that exist that cannot in principle be attributed to selection. It’s not an argument from igorance, but a proof by contradiction.

  16. to reiterate what Sal has alluded to, non-functional Junk DNA is not so much ‘predicted’ by Darwinism as it is ‘required’ by it. i.e. No Junk, No Darwinism!

    Junk DNA Predictions By Leading Evolutionists

    Haldane’s Dilemma
    Excerpt: Haldane was the first to recognize there was a cost to selection which limited what it realistically could be expected to do. He did not fully realize that his thinking would create major problems for evolutionary theory. He calculated that in man it would take 6 million years to fix just 1,000 mutations (assuming 20 years per generation).,,, Man and chimp differ by at least 150 million nucleotides representing at least 40 million hypothetical mutations (Britten, 2002). So if man evolved from a chimp-like creature, then during that process there were at least 20 million mutations fixed within the human lineage (40 million divided by 2), yet natural selection could only have selected for 1,000 of those. All the rest would have had to been fixed by random drift – creating millions of nearly-neutral deleterious mutations. This would not just have made us inferior to our chimp-like ancestors – it surely would have killed us. Since Haldane’s dilemma there have been a number of efforts to sweep the problem under the rug, but the problem is still exactly the same. ReMine (1993, 2005) has extensively reviewed the problem, and has analyzed it using an entirely different mathematical formulation – but has obtained identical results.
    John Sanford PhD. – “Genetic Entropy and The Mystery of the Genome” – pg. 159-160

    Kimura’s Quandary
    Excerpt: Kimura realized that Haldane was correct,,, He developed his neutral theory in responce to this overwhelming evolutionary problem. Paradoxically, his theory led him to believe that most mutations are unselectable, and therefore,,, most ‘evolution’ must be independent of selection! Because he was totally committed to the primary axiom (neo-Darwinism), Kimura apparently never considered his cost arguments could most rationally be used to argue against the Axiom’s (neo-Darwinism’s) very validity.
    John Sanford PhD. – “Genetic Entropy and The Mystery of the Genome” – pg. 161 – 162

    A graph featuring ‘Kimura’s Distribution’ being ‘properly used’ is shown in the following video:

    Evolution Vs Genetic Entropy – Andy McIntosh – video
    http://www.metacafe.com/watch/4028086

    At the 2:45 minute mark of the following video, the mathematical roots of the junk DNA argument, that is still used by many Darwinists, can be traced through Haldane, Kimura, and Ohno’s work in the late 1950’s, 60’s through the early 70’s:

    What Is The Genome? It’s Not Junk! – Dr. Robert Carter – video – (Notes in video description)
    http://www.metacafe.com/w/8905583

    Kimura (1968) developed the idea of “Neutral Evolution”. If “Haldane’s Dilemma” is correct, the majority of DNA must be non-functional.

    The slow, painful death of junk DNA:
    Junk DNA is not just a label that was tacked on to some DNA that seemed to have no function; it is something that is required by evolution. Mathematically, there is too much variation, too much DNA to mutate, and too few generations in which to get it all done. This was the essence of Haldane’s work….Junk DNA is a necessary mathematical extrapolation…Without Junk DNA, evolution runs into insurmountable mathematical difficulties.
    http://creation.com/junk-dna-slow-death

    Susumu Ohno, a leader in the field of genetics and evolutionary biology, explained in 1972 in an early study of non-coding DNA that, “they are the remains of nature’s experiments which failed. The earth is strewn with fossil remains of extinct species; is it a wonder that our genome too is filled with the remains of extinct genes?”

    Richard Sternberg, who has a PhD. in Evolutionary Biology, traces how the junk DNA argument developed through the mid 1970’s to the early 80’s and beyond in the following article:

    How The Junk DNA Hypothesis Has Changed Since 1980 – Richard Sternberg – October 8, 2009
    Excerpt: Two papers appeared back to back in the journal Nature in 1980: “Selfish Genes, the Phenotype Paradigm and Genome Evolution” by W. Ford Doolittle and Carmen Sapienza and “Selfish DNA: The Ultimate Parasite” by Leslie Orgel and Francis Crick. These laid the framework for thinking about nonprotein-coding regions of chromosomes, judging from how they are cited. What these authors effectively did was advance Dawkins’s 1976 selfish gene idea in such a way that all the genomic DNA evidence available up to that time could be accounted for by a plausible scenario. The thesis presented in both articles is that the only specific function of the vast bulk of “nonspecific” sequences, especially repetitive elements such as transposons, is to replicate themselves — this is the consequence of natural selection operating within genomes, beneath the radar of the cell. These junk sequences, it was postulated, can duplicate and disperse throughout chromosomes because they have little or no effect on the phenotype, save for the occasional mutation that results from their mobility.
    http://www.evolutionnews.org/2.....26421.html

  17. Eric Anderson,

    Lot’s of evolutionary biologists have given estimates for the amount of junk DNA. I think it’s unlikely that much more than 10% of the genome is functional in meaningful sense, and that’s after reading the ENCODE papers (well, the big ones). Have you read them? Do you understand what the definition of “functional” is for the classes ENCODE uses?

  18. Well wd400 it is a given that natural selection doesn’t do anything in a meaningful sense. Can you reference any evidence that your position’s mechanisms can construct something functional, in a meaningful sense?

    But anyway- are there species with little to no junk DNA? Are there varying degrees from “lots” to “zero”? Does “evolution” explain all of that from lots to zero? Then it explains nothing…

  19. Are you sure that ‘functional’ means what you think it means? And, if it does, do you really want to adopt this definition of function consistently in biological discussions?

    Mung in #3 asks, “isn’t it a claim of modern evolutionary theory that we can reliably determine evolutionary relationships from sections of non-functional DNA precisely because they are non-functional?”

    Neutrally evolving sequences are certainly useful in estimating phylogeny, but ENCODE’s definition tells us nothing about whether sequences are freely accumulating mutations, or if they are tightly constrained by evolution.

    Now, every bp in every intron is ‘functional’ under ENCODE’s definition, simply because they are initially transcribed – not because they “do something” for the organism or have any actual biological consequence. This is not what ‘functional’ means to most people (hence the errant claims about the death of junk DNA – again – in the media). ENCODE’s definition of functional tells us exactly nothing about the biological necessity of such sequences or how they evolve, only that on some level they show evidence of biological activity. Hence the bar is very low: ENCODE still only have evidence of function under traditional definitions in 9% of the genome – which is what was predicted long before ENCODE began.

    The coordinator of ENCODE has quite a telling discussion about this on his blog.

  20. Joe,

    Yeah, actually, evolutionary can explain quite a lot of variation in genome-size and genome-junkiness. Selection is a weaker force in small populations than large ones, since a little extra junk DNA is likely to be nearly-neutral in a small population we can’t control it.

    There are many other things that contribute to the junkiness of a genome, and some of them are probable historical accidents. It’s quite an interesting question when you take an evidence-based approach to it – you should try that out.

  21. wd400-

    Yeah, it explains everything. even the stuff that surprises the heck out of biologists. BTW evolution is supposedly all historical accidents- nothing was planned.

    As for an evidenced-based approach, well that is why I infer Intelligent Design.

  22. paulmc-

    Introns ARE functional- ie they do something for the organism- they allow for alternative gene splicing. Take them out and see what happens. And blind and undirected processes can’t account for any level of biological activity. So your position still has some ‘splainin’ to do…

  23. Firstly, a few dozen base pairs are needed for alternative splicing, not entire introns (typical length: 3500 bp). Secondly, few genes reliably produce multiple transcripts, so their introns do not function (except in the ENCODE sense). Thirdly, of those that do produce an additional transcript, an exon is usually skipped – yet a typical human gene has eight introns, meaning most introns are not involved in producing alternative mRNAs even in genes that do exhibit alternative splicing.

  24. Hey paulmc,

    Even though I take the ID side, but I wanted to thank you for coming here to engage us in debate. It would be a boring monoculture without dissenting opinions :)

  25. Paul,

    I see what you are saying. And I think it’s probably true. But, do you know what it teaches me? With words like junk be ascribed to “somewhat functional DNA” and function being ascribed to ” somewhat functional DNA” that scientists SUCK at the English language. This is ridiculous, why would ANYONE use the words Junk when it has function? Even if it is a little bit…and why would these scientists use the words “80 percent functional” if it’s not really. Scientists really need some help with their correct word usages. For the commoner like myself, it’s no wonder we have a hard time understanding this kind of literature, it’s just like the news!

  26. On junk-DNA I’ve been called a liar for Jesus by many. 6 September 2012 I can finally say….. I told you so!

  27. paulmc- future uses, as I told you before. As I said you don’t understand how to design and how to design such that you have viable and helpful variation for possible future requirements.

    Just because YOU don’t understand the design requirement for introns does not mean there isn’t one.

    YOUR position can’t explain introns nor alternative gene splicing. So perhaps you guys should focus on your position for a while, at least until you can get it sorted out.

    How many proteins does the human genome produce vs how many genes?

  28. paulmc, good to see you back (and wd400) and to know you are lurking. :)

    So the evolutionary estimate of “real” function is around 10% and my estimate is 90%+. Hmmm . . . The strange thing is that we already know (per your and wd400′s acknowledgement) of about 10% worth of function. So saying that about 10% (plus or minus a couple points) is functional is asserting that we already have figured out essentially all the functional aspects of DNA. Sorry, but that is just laughable. Particularly when we know there are literally thousands of functions that occur in our bodies for which we have not yet identified the source of the information for that function. A fair amount may be epigentic to be sure, but much is likely genetic in origin.

    Pervasive, massive quantity junk DNA was more believable and made more sense to the evolutionary story when it just sat there quietly behaving itself and did nothing (you know, the whole “neutral” catch-all idea it was largely based on in the first place). Now we know that the vast majority of DNA is transcribed, so here’s your theory: “At least 70% of the entire genome is transcribed, even though it has no function and is complete junk.” Talk about selection pressure! Not only is DNA awash in junk we are told, but now the cell expends massive resources and energy transcribing 7x more junk than functional strings, and is left to deal with all the transcribed junk literally clogging up the cell. That is a pretty remarkable viewpoint and one that is flatly in opposition to the idea that “conserved stuff is conserved because it has function.”

    I know you will stand fast in your belief that DNA is mostly junk, so we probably won’t get anywhere for now. We’ll just keep the friendly bet open. Remember, though, that, by definition, every single discovery of new function moves the needle toward my end of the bet! :)

  29. as to:

    every single discovery of new function moves the needle toward my end of the bet!

    this:

    Francis Collins, Darwin of the Gaps, and the Fallacy Of Junk DNA – video
    http://www.evolutionnews.org/2.....40361.html

    Francis Collins’s Junk DNA Arguments Pushed Into Increasingly Small Gaps in Scientific Knowledge – May 2011
    http://www.evolutionnews.org/2.....46251.html

  30. Anyone have any thoughts on this> http://www.genomicron.evolverz.....est-silly/

  31. Anyone have any thoughts on this? (and then you list the onion test)

    My thoughts are that human ignorance for why the genomes are the specific varying sizes they are is not a argument for the Darwinian origin of those specific varying sizes! In fact some very credible reasons have been put forth for why it would make ‘engineering sense’ to vary genome sizes as such:

    i.e. There is no logical ‘evolutionary progression’ to be found for the amount of DNA in less complex animals to the size of genomes found in more complex animals. In fact the genome sizes are known to vary widely between Kinds/Species despite their differences in complexity and this mystery is known as the c-value enigma:

    C-value enigma
    Excerpt: it was soon found that C-values (genome sizes) vary enormously among species and that this bears no relationship to the presumed number of genes (as reflected by the complexity of the organism). For example, the cells of some salamanders may contain 40 times more DNA than those of humans. Given that C-values were assumed to be constant because DNA is the stuff of genes, and yet bore no relationship to presumed gene number, this was understandably considered paradoxical;
    http://en.wikipedia.org/wiki/C-value_enigma

    And yet, even though this C-value enigma is somewhat (very?) paradoxical to the materialistic, neo-Darwinian, point of view, since information is presupposed to simply ‘emerge’ from a material basis and there clearly is no linear correlation to amount of material present and amount of information expressed, from a design point of view we should rightly expect genome sizes to vary within design constraints. Constraints that would obviously be imposed in trying to achieve a ‘optimal design’ for any particular life-form that was designed; For examples of such constraints,,:

    “There is strong positive correlation, however, between the amount of DNA and the volume of a cell and its nucleus – which effects the rate of cell growth and division. Furthermore, in mammals there is a negative correlation between genome size and rate of metabolism. Bats have very high metabolic rates and relatively small genomes. In birds, there is a negative correlation between C-value and resting metabolic rate. In salamanders, there is also a negative correlation between genome size and the rate of limb regeneration.”
    Jonathan Wells – The Myth Of Junk DNA – page 85

    Similarities Found in Genomes Across Multiple Species; Platypus Still out of Place – July 2011
    Excerpt: “Basically what this all means is that if the chromosome number of a species can be given, the relative sizes of all the chromosomes can instantly be known,” Yu said. “Also, if you tell me the genome size in the chromosome base pair, I can tell you the base pair length of each chromosome.”
    http://pos-darwinista.blogspot.....evela.html

    THE ALLOMETRIC RELATIONSHIP BETWEEN GENOME SIZE (C-VALUE) AND TOTAL METABOLIC ENERGY PER LIFESPAN, PER UNIT BODY MASS IN ANIMALS
    Excerpt: this show(s) that,,, the higher total life energy per unit body mass leads to smaller C-value.
    http://www.sustz.com/Proceedin.....ANASOV.pdf

    As well, at the 7:00 minute mark of this following video, we find that ‘genome length vs. mass’ gives a enigmatic 1/4 power scaling on the plotted graph for a wide range of different creatures. Thus, once again, giving strong indication of a design constraint that was/is imposed, top down, on genome length, and which is inexplicable from the neo-Darwinian framework:

    4-Dimensional Quarter Power Scaling In Biology – video
    http://www.metacafe.com/watch/5964041/

    Chargaff’s “Grammar of Biology”: New Fractal-like Rules – 2011
    Excerpt from Conclusion: It was shown that these rules are valid for a large set of organisms: bacteria, plants, insects, fish and mammals. It is noteworthy that no matter the word length the same pattern is observed (self-similarity). To the best of our knowledge, this is the first invariant genomic properties publish(ed) so far, and in Science invariant properties are invaluable ones and usually they have practical implications.
    http://arxiv.org/ftp/arxiv/pap.....2.1528.pdf

    Why the “Onion Test” Fails as an Argument for “Junk DNA” – Jonathan M. – November 2, 2011
    Excerpt: The so-called onion test, or indeed the “C-value enigma,” is predicated on unsupportable assumptions about the physiological effects of — and/or requirements for — larger genomes, many of which are contradicted by the scientific evidence.
    http://www.evolutionnews.org/2.....52321.html

  32. You are all over the place on this one Eric.

    Neutral theory was built on observations about polymorphism – not so much function. These precasive RNAs are not conserved (only about 5% of our genome appears to be subject to negative selection).

    The idea that selection can get rid of every weakly expensive variant is hyper-selectionist (it’s amusing how Dawkins-like most creationists are when they talk about evolution acutally…). What do you think the cost of one more transcript is? Evolution doesn’t give you a chance to compare a pristine genome with a junky one – just the differences between one genome and another. That’s a recipe for a ratchet that could easily end up with a genome that is complex as in bureaucracy not complex as in a machine.

    I just think you have a long way to go form “makes RNA” (as Paul points out that’s every base of every intron!) to “has a function”

  33. wd400 you claim :

    Neutral theory was built on observations about polymorphism

    No it wasn’t:

    Haldane’s Dilemma
    Excerpt: Haldane was the first to recognize there was a cost to selection which limited what it realistically could be expected to do. He did not fully realize that his thinking would create major problems for evolutionary theory. He calculated that in man it would take 6 million years to fix just 1,000 mutations (assuming 20 years per generation).,,, Man and chimp differ by at least 150 million nucleotides representing at least 40 million hypothetical mutations (Britten, 2002). So if man evolved from a chimp-like creature, then during that process there were at least 20 million mutations fixed within the human lineage (40 million divided by 2), yet natural selection could only have selected for 1,000 of those. All the rest would have had to been fixed by random drift – creating millions of nearly-neutral deleterious mutations. This would not just have made us inferior to our chimp-like ancestors – it surely would have killed us. Since Haldane’s dilemma there have been a number of efforts to sweep the problem under the rug, but the problem is still exactly the same. ReMine (1993, 2005) has extensively reviewed the problem, and has analyzed it using an entirely different mathematical formulation – but has obtained identical results.
    John Sanford PhD. – “Genetic Entropy and The Mystery of the Genome” – pg. 159-160

    Kimura’s Quandary
    Excerpt: Kimura realized that Haldane was correct,,, He developed his neutral theory in responce to this overwhelming evolutionary problem. Paradoxically, his theory led him to believe that most mutations are unselectable, and therefore,,, most ‘evolution’ must be independent of selection! Because he was totally committed to the primary axiom (neo-Darwinism), Kimura apparently never considered his cost arguments could most rationally be used to argue against the Axiom’s (neo-Darwinism’s) very validity.
    John Sanford PhD. – “Genetic Entropy and The Mystery of the Genome” – pg. 161 – 162

    A graph featuring ‘Kimura’s Distribution’ being ‘properly used’ is shown in the following video:

    Evolution Vs Genetic Entropy – Andy McIntosh – video
    http://www.metacafe.com/watch/4028086

    Majestic Ascent: Berlinski on Darwin on Trial – David Berlinski – November 2011
    Excerpt: The publication in 1983 of Motoo Kimura’s The Neutral Theory of Molecular Evolution consolidated ideas that Kimura had introduced in the late 1960s. On the molecular level, evolution is entirely stochastic, and if it proceeds at all, it proceeds by drift along a leaves-and-current model. Kimura’s theories left the emergence of complex biological structures an enigma, but they played an important role in the local economy of belief. They allowed biologists to affirm that they welcomed responsible criticism. “A critique of neo-Darwinism,” the Dutch biologist Gert Korthof boasted, “can be incorporated into neo-Darwinism if there is evidence and a good theory, which contributes to the progress of science.”
    By this standard, if the Archangel Gabriel were to accept personal responsibility for the Cambrian explosion, his views would be widely described as neo-Darwinian.
    http://www.evolutionnews.org/2.....53171.html

    Thou Shalt Not Put Evolutionary Theory to a Test – Douglas Axe – July 18, 2012
    Excerpt: “For example, McBride criticizes me for not mentioning genetic drift in my discussion of human origins, apparently without realizing that the result of Durrett and Schmidt rules drift out. Each and every specific genetic change needed to produce humans from apes would have to have conferred a significant selective advantage in order for humans to have appeared in the available time (i.e. the mutations cannot be ‘neutral’). Any aspect of the transition that requires two or more mutations to act in combination in order to increase fitness would take way too long (>100 million years).
    My challenge to McBride, and everyone else who believes the evolutionary story of human origins, is not to provide the list of mutations that did the trick, but rather a list of mutations that can do it. Otherwise they’re in the position of insisting that something is a scientific fact without having the faintest idea how it even could be.” Doug Axe PhD.
    http://www.evolutionnews.org/2.....62351.html

    Here is a Completely Different Way of Doing Science – Cornelius Hunter PhD. – April 2012
    Excerpt: But how then could evolution proceed if mutations were just neutral? The idea was that neutral mutations would accrue until finally an earthquake, comet, volcano or some such would cause a major environmental shift which suddenly could make use of all those neutral mutations. Suddenly, those old mutations went from goat-to-hero, providing just the designs that were needed to cope with the new environmental challenge. It was another example of the incredible serendipity that evolutionists call upon.
    Too good to be true? Not for evolutionists. The neutral theory became quite popular in the literature. The idea that mutations were not brimming with cool innovations but were mostly bad or at best neutral, for some, went from an anathema to orthodoxy. And the idea that those neutral mutations would later magically provide the needed innovations became another evolutionary just-so story, told with conviction as though it was a scientific finding.
    Another problem with the theory of neutral molecular evolution is that it made even more obvious the awkward question of where these genes came from in the first place.
    http://darwins-god.blogspot.co.....ay-of.html

    Darwin’s Legacy – Donald R. Prothero – February 2012
    Excerpt: “For the first decade after the paper [Punctuated Equilibrium] was published, it was the most controversial and hotly argued idea in all of paleontology. Soon the great debate among paleontologists boiled down to just a few central points, which Gould and Eldredge (1977) nicely summarized on the fifth anniversary of the paper’s release. The first major discovery was that stasis was much more prevalent in the fossil record than had been previously supposed. Many paleontologists came forward and pointed out that the geological literature was one vast monument to stasis, with relatively few cases where anyone had observed gradual evolution. If species didn’t appear suddenly in the fossil record and remain relatively unchanged, then biostratigraphy would never work—and yet almost two centuries of successful biostratigraphic correlations was evidence of just this kind of pattern. As Gould put it, it was the ‘dirty little secret’ hidden in the paleontological closet. Most paleontologists were trained to focus on gradual evolution as the only pattern of interest, and ignored stasis as ‘not evolutionary change’ and therefore uninteresting, to be overlooked or minimized. Once Eldredge and Gould had pointed out that stasis was equally important (‘stasis is data’ in Gould’s words), paleontologists all over the world saw that stasis was the general pattern, and that gradualism was rare—and that is still the consensus 40 years later. …
    In my dissertation on the incredibly abundant and well preserved fossil mammals of the Big Badlands of the High Plains, I had over 160 well-dated, well-sampled lineages of mammals, so I could evaluate the relative frequency of gradualism versus stasis in an entire regional fauna. …
    it was clear that nearly every lineage showed stasis, with one minor example of gradual size reduction in the little oreodont Miniochoerus. I could point to this data set and make the case for the prevalence of stasis without any criticism of bias in my sampling. More importantly, the fossil mammals showed no sign of responding to the biggest climate change of the past 50 million years (the Eocene-Oligocene transition, when glaciers appeared in Antarctica after 200 million years). In North America, dense forests gave way to open scrublands, crocodiles and pond turtles were replaced by land tortoises, and the snails changed from those typical of Nicaragua to those of Baja California. Yet out of all the 160 lineages of mammals in this time interval, there was virtually no response.”,,,
    In four of the biggest climatic-vegetational events of the last 50 million years, the mammals and birds show no noticeable change in response to changing climates. No matter how many presentations I give where I show these data, no one (including myself) has a good explanation yet for such widespread stasis despite the obvious selective pressures of changing climate.
    http://www.skeptic.com/eskeptic/12-02-15/#feature

  34. …the neutral theory regards protein and DNA polymorphisms as a transient phase of molecular evolution and rejects the notion that the majority of such polymorphisms are adaptive and maintained in the species by some form of balancing selection.
    – Motoo Kimura

    So yes, I think wd400 has a point.

  35. …I don’t usually read the BA spam. But even the mutational load argument is about among-species polymorphism (that there are more of them than we’d expect if selectoin was responsible for most changes), not function, which is the error Eric made and I was trying to correct.

  36. So yes, I think wd400 has a point.

    In so far that neutral theory has any point worth considering, it is the fact that neutral theory makes it clear that Darwinism is complete pseudo-scientific tripe that refuses to submit to any rigid falsification criteria!

  37. lol. What do you think neutral theory is BA?

  38. as to:

    …the neutral theory regards protein and DNA polymorphisms as a transient phase of molecular evolution,,,

    Huge problem, there is no evidence that protein ‘polymorphisms’ are ‘transient’!:

    Following the Evidence Where It Leads: Observations on Dembski’s Exchange with Shapiro – Ann Gauger – January 2012
    Excerpt: So far, our research indicates that genuine innovation, a change to a function not already pre-existent in a protein, is beyond the reach of natural processes, even when the starting proteins are very similar in structure.
    http://www.evolutionnews.org/2.....55171.html

    Wheel of Fortune: New Work by Thornton’s Group Supports Time-Asymmetric Dollo’s Law – Michael Behe – October 5, 2011
    Excerpt: Darwinian selection will fit a protein to its current task as tightly as it can. In the process, it makes it extremely difficult to adapt to a new task or revert to an old task by random mutation plus selection.
    http://www.evolutionnews.org/2.....51621.html

    Stability effects of mutations and protein evolvability. October 2009
    Excerpt: The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability,,
    http://www.ncbi.nlm.nih.gov/pubmed/19765975

    When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe
    Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied.
    http://www.biologicinstitute.o.....nt-collide

    Why Proteins (Protein Domains) Aren’t Easily Recombined – Ann Gauger – May 2012
    Excerpt: each particular helix or sheet has a distinct set of side chains sticking out from it, requiring a distinct set of chemical interactions with any nearby protein sequence. Thus, helices and sheets are sequence-dependent structural elements within protein folds. You can’t swap them around like lego bricks. This necessarily means that when you bring new secondary structure elements into contact by some sort of rearrangement, they will be unlikely to form a stable three dimensional fold without significant modification.
    http://www.biologicinstitute.o.....recombined

    “Why Proteins Aren’t Easily Recombined, Part 2″ – Ann Gauger – May 2012
    Excerpt: “So we have context-dependent effects on protein function at the level of primary sequence, secondary structure, and tertiary (domain-level) structure. This does not bode well for successful, random recombination of bits of sequence into functional, stable protein folds, or even for domain-level recombinations where significant interaction is required.”
    http://www.biologicinstitute.o.....ned-part-2

  39. lol. What do you think neutral theory is BA?

    science fiction!

    Tell you what wd400, let’s quit playing games and just cut to the chase, and you go ahead and produce actual evidence for Darwinian evolution producing just one molecular machine? I know I will be waiting a long time for you to produce any substantiating evidence, since you have no actual evidence,

    “There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject.”
    James Shapiro – Molecular Biologist

    and you will try to play stupid games instead of producing actual evidence (because Darwinism is not about what the evidence actually says for you is it?),, but on the other hand I can produce actual evidence of Intelligence producing a molecular machine:

    (Man-Made) DNA nanorobot – video
    https://vimeo.com/36880067

    Why do you play games wd400?

  40. I’m not the one playing games. You did whatever it is that you did to create these copy-paste-spam things without even understanding what neutral theory is (as far as I can tell). (Nearly) Neutral theory is pretty relevent to the ENCODE results, so it would be good if you understood it.

  41. wd400:

    You’re missing the point. How is it possible that there is so much junk DNA hanging around in our genome for generations? Certainly not because it is being selected for. Instead precisely because, so the thinking goes, it is neutral.

    The idea of vast amounts of junk DNA in the genome was at least made more believable and palatable by the idea that it was neutral. As long as it sat there and minded its own business there could be tons of it — the cell wouldn’t care.

    The idea that selection can get rid of every weakly expensive variant is hyper-selectionist . . . What do you think the cost of one more transcript is?

    Now, however, we know that it doesn’t just sit there. It gets transcribed. Pervasively so. So now we are being asked to believe that the vast majority of the transcription work in the cell (7/8th of the genome), and the subsequent sorting, breakdown and recycling work of all those RNA strands, is utterly, completely, without function and useless. In fact it is much worse than useless. It uses up much of the cell’s transcription and RNA recycling work. I’m certainly not being hyper-selectionist. I have never argued that 100% of DNA has function. No-one is talking about “one more transcript.” We’re talking about the vast majority of the genome.

    So are you really going to stick with the position that fully 70% of the genome is transcribed (with all that entails in terms of materials and transcription resources, later sorting and identification of RNA strands, breakdown, etc.), even though it is utterly, completely useless? And that such a massive use of resources would not result in any selection pressure? And that it would not interfere in any way with the small transcribed amount that is functional? Sorry, but that is just laughable.

    And based on what evidence? That we haven’t identified a particular function yet? I don’t get it. Even if you don’t accept design, why fight so tooth and nail against the idea of more DNA function? Why not embrace new developments as interesting evidence that might lead us to understand more about how much function DNA really has?

  42. read what I said. You can’t compare a pristine junk-free genome to a very junky one, because evolution would never get that chance.

    I don’t really think junk DNA has much to say on design, but I do fight against the sort of mischracterisation of the genome that sees it as a well oiled machine.

  43. So no actual evidence (a molecular machine) to support your position, and then, ironically, right after presenting no actual evidence for your position, you issue a denial that you are playing games! Dog, Tail, Chase! Then after such blatant inanity, you state:

    it would be good if you understood it.

    I understand it well enough to know that Dr. Sanford has rigorously shown it to be false.,,, But what I REALLY would like to know is how could you ever truly know if YOU ever understood it to be true if neo-Darwinism were actually true? You simply have no way of establishing 100% certainty in your atheistic/materialistic worldview

    Self-Refuting Belief Systems – Cornelius Hunter – September 2012
    Excerpt: Relativism states that there are no absolute truths, but if true then that statement is an absolute truth. Likewise the statement that evolution is a fact, if true, means that we cannot know evolution to be a fact. Why? Because with evolution our minds are nothing more than molecules in motion—an accidental biochemistry experiment which has yielded a set of chemicals in a certain configuration. This leads to what Darwin called “the horrid doubt”:
    “But then with me the horrid doubt always arises whether the convictions of man’s mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey’s mind, if there are any convictions in such a mind.” Darwin to Graham, William – 3 July 1881
    Today evolutionists agree that while a random collection of chemicals doesn’t know anything, nonetheless over long time periods and under the action of natural selection, phenomena which we refer to as knowledge, will and consciousness will spontaneously emerge. And how do we know this? Because evolution occurred and we know that it occurred. Therefore evolution must have created the phenomena of knowledge. The proof is left to the student.
    http://darwins-god.blogspot.co.....stems.html

    The following interview is sadly comical as a evolutionary psychologist realizes that neo-Darwinism can offer no guarantee that our faculties of reasoning will correspond to the truth, not even for the truth that he is purporting to give in the interview, (which begs the question of how was he able to come to that particular truthful realization, in the first place, if neo-Darwinian evolution were actually true?);

    Evolutionary guru: Don’t believe everything you think – October 2011
    Interviewer: You could be deceiving yourself about that.(?)
    Evolutionary Psychologist: Absolutely.
    http://www.newscientist.com/ar.....think.html

    Related article:

    Evolutionists Are Now Saying Their Thinking is Flawed (But Evolution is Still a Fact) – Cornelius Hunter – May 2012
    Excerpt: But the point here is that these “researchers” are making an assertion (human reasoning evolved and is flawed) which undermines their very argument. If human reasoning evolved and is flawed, then how can we know that evolution is a fact, much less any particular details of said evolutionary process that they think they understand via their “research”?
    http://darwins-god.blogspot.co.....their.html

    Modern science was conceived, and born, and flourished in the matrix of Christian theism. Only liberal doses of self-deception and double-think, I believe, will permit it to flourish in the context of Darwinian naturalism.
    ~ Alvin Plantinga

    Epistemology – Why Should The Human Mind Even Be Able To Comprehend Reality? – Stephen Meyer – video – (Notes in description)
    http://vimeo.com/32145998

  44. wd400:

    …I don’t usually read the BA spam.

    BA sort of operates in his own sphere. Mostly I am content to just let him do his thing (he’s ID friendly, so am I. I think he’s a believer, so am I – sure, I’ll admit the bias). But sometimes, when scrolling down a page, trying as I might not to wade though all the copy-paste-spam, something catches my eye that makes me say, HUH?

    I can’t tell you how long it’s been since I’ve had Kimura’s book in front of me, but that thing about polymorphism’s struck a nerve, so I checked …

  45. How much you want to bet Salvador has even posted on the subject, lol? That’s really testing my memory.

  46. Mung, the point on neutral theory NOT being based on ‘observation of ‘transient’ polymorphisms’ is, as far as I can tell, valid since there is in fact no observational evidence that ‘transient’ proteins exist.

    i.e. wd400 claimed:

    “Neutral theory was built on observations about polymorphism”

    and you cited:

    …the neutral theory regards protein and DNA polymorphisms as a transient phase of molecular evolution,,,

    ,,,Thus since there is no observational evidence of ‘transient polymorphisms’ then the claim is irrelevant, or worse yet, a lie! Moreover, my references from Sanford stand unchallenged even though they should shut the debate down if unchallenged!

  47. BA,

    “Transient proteins” and “transient DNA” and “transient polymorphisms” are your own straw-man constructs.

    How did Kimura know about polymorphisms, whether in DNA or proteins, without observations?

    Why do you place ‘transient polymorphisms’ in quotes? Who are you quoting?

    fyi, I do not claim that polymorphisms were the sole basis for the neutral theory. Anyone who has actually read Kimura would know better.

    But you completely poo-poo the idea, and you’re wrong. You do no favors for the cause of ID by denying evident facts.

    I’ve both defended and criticized Sanford. So what do you hope to gain there?

  48. BA,

    This will be my last, but what do you think a “transient” protein is? The transient polymprophisms those profoundly non-Darwinian evolutionary biologists Kimura, Ohto and Nei were talking about were variant that come into a population, stick around and perhaps even fix without having any impact on their hosts survival. There is quite of of evidence that this sort of thing is common.

  49. it was discovered that, even though the vast majority of our DNA does not code for proteins, the human genome is nonetheless pervasively transcribed into mRNA.

    Um, that’s not what was discovered.

    Jonathan M, do you know what mRNA is? Just wondering.

  50. wd400 you claim:

    “There is quite (A lot) of evidence that this sort of thing is common.”

    really??? you got (a lot) of evidence??? Please do provide a detailed amino acid by amino acid, step by step, ‘trivial’ transition of a single protein to a novel variant.

    When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe
    Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied.

    ,,,Mung please cite the actual observational evidence that led Kimura to believe that these DNA and Protein polymorphisms were transient (as you yourself cited!). Myself, regardless of what you personally think of me, I have much observational evidence gathered that argues very strongly for constraint of protein evolvability.

  51. JLAfan says:

    “This is yet another prediction verified for evolution through common ancestry.”

    Well, I think it is far too early to make that kind of a claim. Let’s wait and see how this all pans out. There is still so much unknown about the genome. It has many more surprises for us.

    This result certainly fits with ID much better than with evolution and common descent. For instance, Jonathan M over at Evolution News and Views wrote this in an article stating why this is such a big deal:

    “the prized 98% sequence-identify figure between humans and chimpanzees relates to the 2% of DNA that codes for the production of proteins. The non-protein-coding regions of DNA are far more species-specific. If these stretches of non-coding DNA really are functional, then what becomes of this sequence-identity figure and its significance with respect to shared ancestry?”

    Here, courtesy of crev dot info, is a very interesting statement from the article in the Wall St. Journal entitled Junk DNA’ debunked”,

    “The unexpected level of activity seen in the genomic hinterlands may also help explain what makes us human. Compared with other species, the human genome has about 30 times as much “junk DNA.””

    If this is true, wouldn’t you say it has absolutely huge implications for the chimp to man evolutionary story? I mean, come on, we’re talking 30 times more regulatory elements than animals, including chimps! I don’t know what kind of a percentage difference this will turn out to be, but one thing is for sure, it is no where close to the 98% story that evolutionists have been using as evidence to support common descent!

    If I am understanding this properly, this would indicate a vast impassable gap between us and chimps, especially given the evolutionary timeline that only allows, what — something like only 6 million years or so for the change from apes to man to have taken place? Simply impossible.

    I’ll look forward to the implications of this research as more is learned, evaluated, and published. I think it is going to make the chimp to human idea sound absolutely incredible!

  52. wd400:

    I don’t really think junk DNA has much to say on design . . .

    I agree with you that both paradigms can accommodate a degree of function and junk. So it is really a question of degree and the overall expectations and weight of the evidence.

    . . . but I do fight against the sort of mischracterisation of the genome that sees it as a well oiled machine.

    That’s OK. I like to fight against the sort of mischaracterization that says a well-oiled system at the macro level can exist and function on the basis of a sea of junk at the micro level. :)

    Now that I think about it, however, such an idea is consistent with the general engineering naivete that characterizes the whole materialist creation story: we have a bunch of chemicals floating around making a mess of things, but voila, out of the chaos emerges life, organisms, functional cellular systems, etc. As long as we don’t ask too many detailed questions about what is really required for a functionally-integrated system to operate, we can cock our head to the side, squint real hard, and kind of imagine that exquisite function ‘just happens’ to emerge from the chaos . . .

  53. wd400:

    I do fight against the sort of mischracterisation of the genome that sees it as a well oiled machine.

    quoted from crev dot info

    Nature looked back at a quote by Nobel laureate David Baltimore 11 years ago when the human genome was first published: “Unless the human genome contains a lot of genes that are opaque to our computers, it is clear that we do not gain our undoubted complexity over worms and plants by using many more genes. Understanding what does give us our complexity — our enormous behavioural repertoire, ability to produce conscious action, remarkable physical coordination (shared with other vertebrates), precisely tuned alterations in response to external variations of the environment, learning, memory … need I go on? — remains a challenge for the future.”

    Hmm. What evidence would it take to convince you? I think the genome works very much like a well oiled machine! Perhaps it has suffered a little rust over time, but it still works quite well, as the prospering of our race would seem to indicate. Is devolution really evidence against it originally having been an even better well oiled machine? Not in my book. Mutations build up over time, but that is to be expected as natural selection just cannot keep up with them all, especially the ones that are not serious enough to warrant being selected for.

    Was it in the original article on Evolution News & Views where they mentioned that even the precise way that DNA folds into a ball and is stored in the cell is important for it’s function? Absolutely amazing. The fold is anything but random and it seems like it would have had to be like that from the beginning.

  54. Dr. Fazale Rana has a short video up on the ENCODE findings:

    Encode DNA Project May Revolutionize Biology – video
    http://www.youtube.com/watch?v=BqcgM9cGxik

  55. Here is another video on the ENCODE announcement:

    ENCODE: The Encyclopedia of DNA Elements (Interviews with members of the ENCODE Project) – video
    http://www.youtube.com/watch?v=PsV_sEDSE2o
    Quotes from preceding video:
    “Very little of our genomes are junk. 80% of our genome is engaged in at least one biochemical activity. For a large fraction of our genome, not now 5%, but 80% of the genome, we can (now) say that we know that it does something.”
    “This metaphor about Junk DNA has become very entrenched. It has been entrenched publically and entrenched scientifically. And ENCODE totally challenges that. We just don’t big, blank, boring, bits of the genome. All the genome is alive at some level.”
    “There are about 2000 DNA binding proteins in the genome. We looked at about 100 of those, 115 of those, so there is a long way to go yet, there is a lot more to study.”

  56. “ENCODE Project Finds Mass Functionality for “Junk” DNA” – podcast
    http://intelligentdesign.podom.....0_13-07_00

  57. Jonathan M- Arthur Hunt, #49, is right. Please correct your OP. Just get rid of the “m” of “mRNA” in your first sentence and add an “s” at the end.

    And if you want you can put a “x” in front to designate different types of RNAs.

    Thank you

  58. tjguy

    “If this is true, wouldn’t you say it has absolutely huge implications for the chimp to man evolutionary story? I mean, come on, we’re talking 30 times more regulatory elements than animals, including chimps! I don’t know what kind of a percentage difference this will turn out to be, but one thing is for sure, it is no where close to the 98% story that evolutionists have been using as evidence to support common descent!”

    Thank you for sharing this as I think this will prove to be very interesting indeed.

  59. tjguy:

    If I am understanding this properly, this would indicate a vast impassable gap between us and chimps, especially given the evolutionary timeline that only allows, what — something like only 6 million years or so for the change from apes to man to have taken place? Simply Impossible.

    Good point. Yet a thought nags at me. How would you describe the gap without this evidence? Puny, tiny, easily traversible in 6 million years? Or is it sill big, huge, massive, so improbable as to be essentially impossible.

    I suppose more evidence will convince a few fence-sitters out there. But the committed materialist is already committed to miracle after miracle just to even get past the laugh test. I’m not sure adding a few more zeroes to the improbabilities will convince anyone who is already avoiding the math.

  60. EA

    “I suppose more evidence will convince a few fence-sitters out there. But the committed materialist is already committed to miracle after miracle just to even get past the laugh test. I’m not sure adding a few more zeroes to the improbabilities will convince anyone who is already avoiding the math.”

    How true that is :o)

  61. Eric said:

    Good point. Yet a thought nags at me. How would you describe the gap without this evidence? Puny, tiny, easily traversible in 6 million years? Or is it still big, huge, massive, so improbable as to be essentially impossible.

    Good question. Even if it were 98%, I personally believe it would be essentially impossible by Darwinian means. Even 2% is not pune, tiny, or easily transversible.

    I’m a bit confused myself about something. Perhaps someone can help.

    When we hear talk of epigenetics, is that the same thing as what the ENCODE project found evidence of or is epigenetics something above and beyond even that?

    If I understand it correctly, it is above and beyond even what the ENCODE project found so that would add a whole extra dimension to the differences between apes and humans and further complicate matters – as if it isn’t impossible as it is.

  62. tjguy:

    Thanks for your thoughts.

    In terms of epigenetics, it is a term that is not used completely consistently, so we have to be careful when we see the term used. In a broad sense, though, it is referring to everything outside of the DNA sequence itself (‘epi’ meaning “upon” or “over,” per my handy dictionary; thus that which is in ‘on top of’ or ‘in addition to’ pure genetic sequence). Sometimes people use the term to describe the higher-level structure of DNA beyond the pure sequence. Other times, they are referring to higher structural elements of the cell/organism completely outside of DNA. There is a whole massive layer of information going on outside of the DNA. I like to keep in mind, for example, that the same DNA exists in cells as diverse as our heart, lungs, eyes, and big toe. Thus, by definition, it is not the DNA that causes different higher level structures.

    Indeed, there is a big open question whether all the information for an organism is even contained in the DNA in the first place.

    A chicken-and-egg problem . . .

    Literally.

  63. It’s remarkable to watch the mental acrobatics take place as committed Darwinists seek to dismiss or minimize the results of the ENCODE project. It’s not as if the results came out of BioComplexity. If Doug Axe or Ann Gauger had published these results, I wouldn’t be surprised to see the dismissal of the findings, as they are on the intellectual blacklist due to their support of ID. Isn’t the ENCODE project the product of hundreds of scientists working nearly a decade, publishing their findings in numerous prestigious peer-reviewed journals (usually the litmus test for what is “scientific”)? What, then, is the problem? This is a striking example of what happens when the Darwinian worldview crashes up against an uncooperative reality. Nick Matzke, paulmc, etc. seem utterly unwilling to discard the hopelessly discredited idea that 90% (or whatever large percentage one may fancy) of the genome is garbage, the leftovers of evolution’s hit-or-miss whimsy. To maintain a semblance of sensibility, such persons have to resort to semantic games (e.g. “what is the definition of functional?”). This a rhetorical strategy that grows evermore hackneyed with each deployment. This same thing happened when ID proponents really started emphasizing the implications of information in DNA. What were previously uncontroversial facts (there’s digital information in DNA, the genetic code is arbitrary, etc. ) were attacked energetically by Darwinists who couldn’t cope with the straightforward inferences that these facts mandated.

    ENCODE aside, did it ever really make sense to conclude that most of the genome is nonfunctional? I would contend that it was never really a logical conjecture to make. How on earth could an organism that comprises some 100 trilion cells, exhibits mechanical complexity on both the micro and the macro level, and possesses the most sophisticated computing system in the known universe (i.e. the brain) be derived from a set of blueprints that is mostly junk? Could an automobile be successfully fashioned by such means? A hand calculator? A typewriter? What seems hopelessly absurd in any other context is par for the course in the magnificent neo-Darwinian synthesis.

    One last thing – enough with the ‘onion test’! Yes it’s odd, no we have no sure explanation for the present, but nonetheless the default fallback of “look at how weird this is, therefore Darwinian evolution must be the cause” is intellectually lazy and a non-sequitir.

  64. My word Optimus,

    Do you know what ENCODE counts as biochemically functional?

    Do you realise that non-Darwinian mechanisma are the reason so much of our genome is junk?

    Do you have an answer to the onion test? Or can you explain why it’s not relevant?

  65. Well, I read the chief researchers’ comments on the presentation, and I read the main Nature paper, and the big story was “Far more of the non-coding genome has control function than we ever dreamed, and most of the rest (possibly nearly all) has some function, the significance, or not, of which is as yet still unknown.”

    So why does all the discussion argue to and from about what is, as yet, unknown, rather than about the highly significant increase in what is known, which flatly contradicts the “junk DNA” hypothesis that only a tiny percentage of introns have “significant” function? That surprise is what the prestigious research team emphasise, and it has many implications worthy of discussion.

    The other 60% or whatever will reveal its secrets by and by. Who knows, the bloated nature of the onion genome might even prove to be a rare and instructive example of how the cell’s usually rigorous self-maintenance can fail and accumulate junk. After all, the Elephant Man didn’t demonstrate that all human features are, in reality, tumours.

  66. This is for Eric Anderson’s comment, up in 13.
    08 Human vitellogenin psu-gene
    http://www.ncbi.nlm.nih.gov/pm.....ool=pubmed

    They predicted that there would be remnants of the gene in a particular place on the chromosome, they looked there, and they were there. Is that the sort of thing you had in mind?

  67. wd400:

    Do you realise that non-Darwinian mechanisma are the reason so much of our genome is junk?

    Yet darwinism did not predict the existence of junk DNA.

    And yes the onion test has been answered by more than one person providing more than one answer.

  68. @ wd400
    Your comment that non-Darwinian mechanisms account for why so much junk is in the genome simply assumes that which is in doubt. The research done by ENCODE indicates that the genome is not nearly as full of junk as Darwinian zealots would have everyone believe. Regardless of the exact figure they presented, the take-away message (as nicely highlighted by Jon Garvey above) is that way more of the genome is being used than was previously thought. Not only is that significant, but so is the idea that DNA acts in a three-dimensional way that dramatically changes our understanding of how sections of DNA interact with other sections that seem remote (two-dimensionally speaking). I don’t think ENCODE is making the claim that they have elucidated what each and every nucleotide does, but they are giving compelling reason to reject non-function as the starting point.
    As far as the onion test is concerned, I already mentioned (reading comprehension helps) that at present there is no sure answer, though, like Joe mentioned, several persons have proposed ideas. My criticism is that it’s a classic argument from ignorance to point to something like the C-value paradox and automatically conclude that it points to a Darwinian origin for DNA generally speaking. That we don’t know why something is as it is does not furnish adequate reason to prefer a cause with unproven explanatory power (Darwinian evolution) over a cause with amply demonstrated explanatory power (ID).

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